Global Patent Index - EP 3594362 A1

EP 3594362 A1 20200115 - METHOD AND SYSTEMS FOR DETERMINING HAPLOTYPES IN A SAMPLE

Title (en)

METHOD AND SYSTEMS FOR DETERMINING HAPLOTYPES IN A SAMPLE

Title (de)

VERFAHREN UND SYSTEME ZUR BESTIMMUNG VON HAPLOTYPEN IN EINER PROBE

Title (fr)

PROCÉDÉ ET SYSTÈMES PERMETTANT DE DÉTERMINER DES HAPLOTYPES DANS UN ÉCHANTILLON

Publication

EP 3594362 A1 20200115 (EN)

Application

EP 19191482 A 20131021

Priority

  • US 201261717495 P 20121023
  • EP 13786074 A 20131021
  • US 2013065855 W 20131021

Abstract (en)

Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads.

IPC 8 full level

C12Q 1/68 (2018.01); G16B 20/20 (2019.01); C12Q 1/6827 (2018.01); C12Q 1/6853 (2018.01); C12Q 1/6874 (2018.01); C12Q 1/6881 (2018.01); C12Q 1/6883 (2018.01); G16B 30/10 (2019.01)

CPC (source: EP US)

C12Q 1/6827 (2013.01 - EP US); C12Q 1/6853 (2013.01 - EP US); C12Q 1/6874 (2013.01 - EP US); C12Q 1/6881 (2013.01 - EP US); C12Q 1/6883 (2013.01 - EP US); G16B 15/00 (2019.01 - EP US); G16B 20/20 (2019.01 - EP US); G16B 30/00 (2019.01 - EP US); G16B 30/10 (2019.01 - EP US); C12Q 2600/172 (2013.01 - EP US)

Citation (applicant)

Citation (search report)

  • [XYI] WO 9835059 A1 19980813 - HILDEBRAND WILLIAM H [US], et al
  • [XYI] US 2010261189 A1 20101014 - BENTLEY GORDON [US], et al
  • [XY] US 2010086914 A1 20100408 - BENTLEY GORDON [US], et al
  • [Y] WO 2005017652 A2 20050224 - ROSETTA INPHARMATICS LLC [US], et al
  • [A] WO 02097047 A2 20021205 - DNAPRINT GENOMICS INC [US], et al
  • [XP] CHANG LIU, YANG XIAO, BRIAN DUFFY ET AL.: "High Resolution HLA Typing by Next Generation Exome Sequencing -- Liu et al. 120 (21): 4166 -- ASH Annual Meeting Abstracts", BLOOD, 1 November 2012 (2012-11-01), XP055089258, Retrieved from the Internet <URL:http://abstracts.hematologylibrary.org/cgi/content/abstract/120/21/4166?maxtoshow=&hits=10&RESULTFORMAT=&fulltext=high+resolution+hla&searchid=1&FIRSTINDEX=0&volume=120&issue=21&resourcetype=HWCIT> [retrieved on 20131120]
  • [IP] KAZUYOSHI HOSOMICHI ET AL: "Phase-defined complete sequencing of the HLA genes by next-generation sequencing", BMC GENOMICS, BIOMED CENTRAL LTD, LONDON, UK, vol. 14, no. 1, 28 May 2013 (2013-05-28), pages 355, XP021151977, ISSN: 1471-2164, DOI: 10.1186/1471-2164-14-355
  • [YP] JOHN KIM HYUNSUNG ET AL: "HLA Haplotyping from RNA-seq Data Using Hierarchical Read Weighting", PLOS ONE, 28 June 2013 (2013-06-28), pages 1 - 10, XP055089263, Retrieved from the Internet <URL:http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0067885&representation=PDF> [retrieved on 20131120]
  • [XI] G. BENTLEY ET AL: "High-resolution, high-throughput HLA genotyping by next-generation sequencing", TISSUE ANTIGENS, vol. 74, no. 5, 1 November 2009 (2009-11-01), pages 393 - 403, XP055087325, ISSN: 0001-2815, DOI: 10.1111/j.1399-0039.2009.01345.x
  • [XYI] BAIYU ZHOU AND ALICE S WHITTEMORE ED - BAIYU ZHOU AND ALICE S WHITTEMORE: "IMPROVING SEQUENCE-BASED GENOTYPE CALLS WITH LINKAGE DISEQUILIBRIUM AND PEDIGREE INFORMATION", THE ANNALS OF APPLIED STATISTICS,, vol. 6, no. 2, 1 June 2012 (2012-06-01), pages 457 - 475, XP002779761
  • [Y] FUERNKRANZ J: "TOP-DOWN PRUNING IN RELATIONAL LEARNING", PROCEEDINGS EUROPEAN CONFERENCE ON ARTIFICIAL INTELLIGENCE, CHICHESTER, GB, 8 August 1994 (1994-08-08), pages 453 - 457, XP000602684
  • [Y] ITSIK PE'ER, JACQUES S. BECKMANN: "Resolution of Haplotypes and Haplotype Frequencies from SNP Genotypes of Pooled Samples", ACM, 2 PENN PLAZA, SUITE 701 - NEW YORK USA, vol. RECOMB, 10 April 2003 (2003-04-10) - 13 April 2003 (2003-04-13), pages 237 - 245, XP040145659

Designated contracting state (EPC)

AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR

DOCDB simple family (publication)

US 2014114579 A1 20140424; US 9181583 B2 20151110; AU 2013334958 A1 20150528; AU 2013334958 B2 20181115; AU 2019200319 A1 20190207; AU 2019200319 B2 20210408; CA 2889507 A1 20140501; CA 2889507 C 20230725; EP 2912192 A1 20150902; EP 2912192 B1 20191009; EP 3594362 A1 20200115; US 10262104 B2 20190416; US 2016098518 A1 20160407; WO 2014066217 A1 20140501

DOCDB simple family (application)

US 201313790112 A 20130308; AU 2013334958 A 20131021; AU 2019200319 A 20190117; CA 2889507 A 20131021; EP 13786074 A 20131021; EP 19191482 A 20131021; US 2013065855 W 20131021; US 201514878830 A 20151008